Saints Row The Third or IV are pretty good options, both support gamepads and the campaigns are fully playable in Co-Op. Issues may arise if one of the two PCs use AMD GPUs though.
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From the ones you have, those that have good critics in term of co-op are Sanctum 2 (haven't tried it myself, so don't take my word for this one, but I did like the single-player),
Sonic & All-Stars Racing Transformed (not exactly Co-op, but can be fun depending on the company),
Left4Dead 1 or 2.
By the way, what gamepad did you get? Xbox One/360 or one from another manufacturer? Just out of curiosity, I'm loving the one I recently got as well (Xbox One).
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Payday 1 and 2. Great coop game. L4D with a good twist :)
Torchlight II. An nice Hack n Slay with a good coop mode.
Diablo 2:LoD and Diablo 3. D2 is the HnS masterpiece and D3:RoS a good followup. should be at least tried.
Borderlands 1 and 2. Grab an classic RPG and mix it with a bit of Steampunk and some FPS. Voilá you got an great Coop game with a breeze of fresh air.
In general i recommend http://www.co-optimus.com/system/4/pc.html for lookin for coop games. it is a great source of information.
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So far I have bought these for my friend (I already had all of them, except Ibb & Obb):
We also play the following games:
Any more recommendations?
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You should play Killing Floor. It's the best game ever ;-)
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I notice you've got all the games from the Humble Co-op Weekly Bundle, maybe pick a game or two from there?
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